Jie Wang1,2,3, Shiming Li2,3, Lei Lan2, Mushan Xie1, Shu Cheng2, Xiaolong Gan4,5, Gang Huang2,3, Guohua Du2, Kang Yu2,3, Xuemei Ni6, Baolong Liu7,8, Guoxiong Peng9. 1. Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China. 2. BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China. 3. BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China. 4. Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China. 5. Key Laboratory of Crop Molecular Breeding, Xining, 810008, Qinghai, China. 6. BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China. nixuemei@genomics.cn. 7. Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China. blliu@nwipb.cas.cn. 8. Key Laboratory of Crop Molecular Breeding, Xining, 810008, Qinghai, China. blliu@nwipb.cas.cn. 9. Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China. gxpeng@cqu.edu.cn.
Abstract
BACKGROUND: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. RESULTS: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. CONCLUSIONS: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.
BACKGROUND:Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. RESULTS: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. CONCLUSIONS: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.
Authors: Thomas P Brutnell; Lin Wang; Kerry Swartwood; Alexander Goldschmidt; David Jackson; Xin-Guang Zhu; Elizabeth Kellogg; Joyce Van Eck Journal: Plant Cell Date: 2010-08-06 Impact factor: 11.277
Authors: Jeffrey L Bennetzen; Jeremy Schmutz; Hao Wang; Ryan Percifield; Jennifer Hawkins; Ana C Pontaroli; Matt Estep; Liang Feng; Justin N Vaughn; Jane Grimwood; Jerry Jenkins; Kerrie Barry; Erika Lindquist; Uffe Hellsten; Shweta Deshpande; Xuewen Wang; Xiaomei Wu; Therese Mitros; Jimmy Triplett; Xiaohan Yang; Chu-Yu Ye; Margarita Mauro-Herrera; Lin Wang; Pinghua Li; Manoj Sharma; Rita Sharma; Pamela C Ronald; Olivier Panaud; Elizabeth A Kellogg; Thomas P Brutnell; Andrew N Doust; Gerald A Tuskan; Daniel Rokhsar; Katrien M Devos Journal: Nat Biotechnol Date: 2012-05-13 Impact factor: 54.908
Authors: Loukas Barton; Seth D Newsome; Fa-Hu Chen; Hui Wang; Thomas P Guilderson; Robert L Bettinger Journal: Proc Natl Acad Sci U S A Date: 2009-03-23 Impact factor: 11.205